removed dist from gitignore so that .jar will be in repo
added Asha's suggested changes: warning if patient has only 1 gene with variants, filtering for pathways with high/low number of genes
fixed boroken iron uptake and transport GPML file
added build instructions, which need to be tested
added usage instructions
adjusting low number of genes warning to be gramatically correct for 0 and 1 genes (currently the threshhold for showing the warning is < 2 genes in variants
added bonferroni/benjamni-hochberg multiple test correction
streamlined GUI so that user cannot click any buttons before choosing a patient, fixed BH multiple test correction
made png files thumbnails instead of full images, and added pathway description panel, and started analysis information tab
used cytoscape's OpenBrowser.java (removed logging) instead of Desktop.getBrowser(), and implemented makeGPMLNodesBlack (still have to give user option to export GPML file)
added export GPML file button
Merge branch 'master' of https://github.com/compbio-UofT/pathways-app